Add package inclusion dir. at the API level

Add package inclusion dir. at the API level

This patch adds a `with_package_inclusion_directory` boolean parameter
(true by default) to the barectf.effective_configuration_file() and
barectf.configuration_from_file() functions.

If this new parameter is true, then the package inclusion directory
(`barectf/include/2` or `barectf/include/3`, depending on the
configuration file's version) is appended to the provided inclusion
directories.

This patch moves this logic from the CLI module to the configuration
modules. It is my understanding that users would want to be able to
include package YAML files using only the API. In `cli.py`,
_parse_args() now simply appends the current working directory, so that
the order stays the same:

1. `--include-dir` options, in order.
2. Current working directory.
3. Package inclusion directory.

Signed-off-by: Philippe Proulx <eeppeliteloop@gmail.com>